If the installation can be scripted and run silently, a startup script is probably your best choice here; all other available options need some system management software (such as Microsoft's System Center Configuration Manager).

When you are dealing with a non-MSI (most likely an .exe) you can use other installers. PDQ Deploy is a free installer that allows you to push MSI, EXE, .BAT, .MSU, .MSP, .CMD, .you_get_the_point. (PDQ Deploy is made by my company).

You can also use SCCM, Tivoli, or many other products for deploying software, but these are a tad pricey (and by a tad I mean a ton).